Molecular Monitoring of Bacterial Community Structure in Long-Aged Nukadoko: Pickling Bed of Fermented Rice Bran Dominated by Slow-Growing Lactobacilli

Journal of Bioscience and Bioengineering

Volumn 104, Issue 6, 2007, Pages 481-489

  Nakayama, Jiro ^a   Hoshiko, Hiroyuki ^a   Fukuda, Mizuki ^a   Tanaka, Hidetoshi ^a   Sakamoto, Naoshige ^a   Tanaka, Shigemitsu ^a   Ohue, Kazutoshi ^b   Sakai, Kenji ^b   Sonomoto, Kenji ^a,c  

^a Kyushu Universitay   (Japan)

^b OITA UNIVERSITY   (Japan)

^c KYUSHU UNIVERSITY   (Japan)

Author keywords

denaturing gradient gel electrophoresis; fermented rice bran; fluorescence; in situ hybridization; lactic acid fermentation; lactobacilli; Lactobacillus acetotolerans; microbiota; nukadoko; quantitative real time polymerase chain reaction; quantitative reverse transcription real time polymerase chain reaction

Indexed keywords

ELECTROPHORESIS; FERMENTATION; FLUORESCENCE; LACTIC ACID; MOLECULAR BIOLOGY; PH; TAXONOMIES;

DENATURING GRADIENT GEL ELECTROPHORESIS; FERMENTED RICE BRAN; IN SITU HYBRIDIZATION; LACTIC ACID FERMENTATION; LACTOBACILLUS ACETOTOLERANS; MICROBIOTA; QUANTITATIVE REAL-TIME POLYMERASE CHAIN REACTION;

BACTERIA;

DNA 16S; LACTIC ACID; RNA 16S;

ARTICLE; BACTERIAL GROWTH; DENATURING GRADIENT GEL ELECTROPHORESIS; FERMENTATION; FLUORESCENCE IN SITU HYBRIDIZATION; GENE AMPLIFICATION; GENE CLUSTER; JAPAN; LACTOBACILLUS; LACTOBACILLUS ACETOTOLERANS; LACTOBACILLUS ACIDIFARINAE; MICROBIAL COMMUNITY; MICROBIAL METABOLISM; MOLECULAR BIOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RICE BRAN; RNA GENE; SEQUENCE ANALYSIS;

COLONY COUNT, MICROBIAL; FERMENTATION; LACTOBACILLUS; ORYZA SATIVA; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

BACTERIA (MICROORGANISMS); LACTOBACILLUS; LACTOBACILLUS ACETOTOLERANS; LACTOBACILLUS ACIDIFARINAE; OTUS;

EID: 38149110361     PISSN: 13891723     EISSN: None     Source Type: Journal    
DOI: 10.1263/jbb.104.481     Document Type: Article

References (25)

1. Imai M., Hirano S., and Aiba M. Aging of "nukadoko": changes in flavor constituents. Nippon Nogeikagaku Kaishi 57 (1983) 1113-1120 (in Chinese)
2. Imai M., Hirano S., and Aiba M. Aging of "nukadoko": changes in microflora and constituents. Nippon Nogeikagaku Kaishi 57 (1983) 1105-1112 (in Chinese)
3. Muyzer G. DGGE/TGGE a method for identifying genes from natural ecosystems. Curr. Opin. Microbiol. 2 (1999) 317-322
4. Ercolini D. PCR-DGGE fingerprinting: novel strategies for detection of microbes in food. J. Microbiol. Methods 56 (2004) 297-314
5. Randazzo C.L., Torriani S., Akkermans A.D., de Vos W.M., and Vaughan E.E. Diversity, dynamics, and activity of bacterial communities during production of an artisanal Sicilian cheese as evaluated by 16S rRNA analysis. Appl. Environ. Microbiol. 68 (2002) 1882-1892
6. Haruta S., Ueno S., Egawa I., Hashiguchi K., Fujii A., Nagano M., Ishii M., and Igarashi Y. Succession of bacterial and fungal communities during a traditional pot fermentation of rice vinegar assessed by PCR-mediated denaturing gradient gel electrophoresis. Int. J. Food. Microbiol. 109 (2006) 79-87
7. van Beek S., and Priest F.G. Evolution of the lactic acid bacterial community during malt whisky fermentation: a polyphasic study. Appl. Environ. Microbiol. 68 (2002) 297-305
8. Meroth C.B., Walter J., Hertel C., Brandt M.J., and Hammes W.P. Monitoring the bacterial population dynamics in sourdough fermentation processes by using PCR-denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 69 (2003) 475-482
9. Meroth C.B., Hammes W.P., and Hertel C. Identification and population dynamics of yeasts in sourdough fermentation processes by PCR-denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 69 (2003) 7453-7461
10. Walter J., Tannock G.W., Tilsala-Timisjarvi A., Rodtong S., Loach D.M., Munro K., and Alatossava T. Detection and identification of gastrointestinal Lactobacillus species by using denaturing gradient gel electrophoresis and species-specific PCR primers. Appl. Environ. Microbiol. 66 (2000) 297-303
11. Songjinda P., Nakayama J., Kuroki Y., Tanaka S., Fukuda S., Kiyohara C., Yamamoto T., Izuchi K., Shirakawa T., and Sonomoto K. Molecular monitoring of the developmental bacterial community in the gastrointestinal tract of Japanese infants. Biosci. Biotechnol. Biochem. 69 (2005) 638-641
12. Nakayama J., Fukui M., Songjinda P., Tanaka S., Kunugi R., and Sonomoto K. Analysis of the composition of the intestinal flora: analysis of intestinal bacterial community by DGGE/TGGE. J. Intestin. Microbiol. 18 (2006) 147-153 (in Chinese)
13. Lane D.J. 16S/23S rRNA sequencing. In: Stackebrandt E., and Goodfellow M. (Eds). Nucleic acid techniques in bacterial systematics (1991), John Wiley and Sons, New York, N.Y. 115-176
14. Gurtler V., and Stanisich V.A. New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 142 Pt 1 (1996) 3-16
15. Maidak B.L., Larsen N., McCaughey M.J., Overbeek R., Olsen G.J., Fogel K., Blandy J., and Woese C.R. The Ribosomal Database Project. Nucleic Acids Res. 22 (1994) 3485-3487
16. Amann R.I., Binder B.J., Olson R.J., Chisholm S.W., Devereux R., and Stahl D.A. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56 (1990) 1919-1925
17. Sakai K., Mori M., Fujii A., Iwami Y., Chukeatirote E., and Shirai Y. Fluorescent in situ hybridization analysis of open lactic acid fermentation of kitchen refuse using rRNA-targeted oligonucleotide probes. J. Biosci. Bioeng. 98 (2004) 48-56
18. Entani E., Masai H., and Suzuki K. Lactobacillus acetotolerans, a new species from fermented vinegar broth. Int. J. Syst. Bacteriol. 36 (1986) 544-549
19. Vancanneyt M., Neysens P., de Wachter M., Engelbeen K., Snauwaert C., Cleenwerck I., van der Meulen R., Hoste B., Tsakalidou E., de Vuyst L., and Swings J. Lactobacillus acidifarinae sp. nov. and Lactobacillus zymae sp. nov., from wheat sourdoughs. Int. J. Syst. Evol. Microbiol. 55 (2005) 615-620
20. Fukuda D., Ando M., Kuroki Y., Nakayama J., and Sonomoto K. Molecular genetic analysis of microbiota in nukadoko. New Food Industry 44 (2002) 7-11 (in Chinese)
21. Wang X., Haruta S., Wang P., Ishii M., Igarashi Y., and Cui Z. Diversity of a stable enrichment culture which is useful for silage inoculant and its succession in alfalfa silage. FEMS Microbiol. Ecol. 57 (2006) 106-115
22. De Vuyst L., and Vancanneyt M. Biodiversity and identification of sourdough lactic acid bacteria. Food Microbiol. 24 (2007) 120-127
23. Kemp P.F., Lee S., and Laroche J. Estimating the growth rate of slowly growing marine bacteria from RNA content. Appl. Environ. Microbiol. 59 (1993) 2594-2601
24. Kerkhof L., and Ward B.B. Comparison of nucleic acid hybridization and fluorometry for measurement of the relationship between RNA/DNA ratio and growth rate in a marine bacterium. Appl. Environ. Microbiol. 59 (1993) 1303-1309
25. Poulsen L.K., Ballard G., and Stahl D.A. Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms. Appl. Environ. Microbiol. 59 (1993) 1354-1360